library(DESeq2)## Loading required package: S4Vectors## Warning: package 'S4Vectors' was built under R version 3.6.3## Loading required package: stats4## Loading required package: BiocGenerics## Loading required package: parallel##
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## intersect, setdiff, setequal, unionlibrary(ContrApption)dds <- readRDS("dev/lncDESeq2Obj.Rds")d <- counts(dds, normalized = TRUE)
d %>% head## AL101116_V1 AL101116_V2 AE032117_V1 AE032117_V2 NM012517_V1
## A1BG-AS1 6.461092 7.314992 5.5821144 5.0103583 7.114612
## A2M-AS1 0.000000 2.980182 2.6794149 3.2010622 2.910523
## A2ML1-AS1 0.000000 1.625554 3.1259841 2.9227090 1.293566
## A2ML1-AS2 0.000000 0.000000 0.8931383 0.2783532 0.000000
## AADACL2-AS1 5.384243 1.083703 0.4465692 2.7835324 0.000000
## AATBC 19.383276 12.462579 10.2710905 11.5516593 12.935659
## NM012517_V2 US082217_V1 US082217_V2 IO092116_V1 IO092116_V2
## A1BG-AS1 9.8573234 4.905338 4.9548106 0.000000 0.00000
## A2M-AS1 3.0000550 5.956481 4.7070701 5.658059 0.00000
## A2ML1-AS1 2.3571860 2.102288 0.9909621 0.000000 0.00000
## A2ML1-AS2 1.2857378 1.051144 0.2477405 0.000000 0.00000
## AADACL2-AS1 0.6428689 1.051144 0.9909621 18.388693 0.00000
## AATBC 19.9289365 9.810675 9.6618807 2.829030 24.62219
## II121416_V1 II121416_V2 NZ022317_V1 NZ022317_V2 MT031317_V1
## A1BG-AS1 5.131470 4.272065 9.7613006 5.506895 8.9124631
## A2M-AS1 3.991143 2.848043 3.0034771 4.589079 3.5649852
## A2ML1-AS1 3.420980 0.000000 0.7508693 1.376724 0.5941642
## A2ML1-AS2 1.140327 0.000000 0.0000000 1.376724 0.0000000
## AADACL2-AS1 2.850816 1.424022 2.2526078 1.376724 1.1883284
## AATBC 8.552449 1.424022 20.2734704 17.438500 25.5490609
## MT031317_V2 AA111716_V1 AA111716_V2 OU031617_V1 OU031617_V2
## A1BG-AS1 12.125417 9.406504 25.7132723 0.00000 0
## A2M-AS1 1.212542 4.180669 0.0000000 0.00000 0
## A2ML1-AS1 0.000000 0.000000 0.0000000 0.00000 0
## A2ML1-AS2 1.212542 0.000000 0.0000000 0.00000 0
## AADACL2-AS1 3.637625 3.135501 0.0000000 0.00000 0
## AATBC 18.188126 11.496839 0.9523434 2.44878 0
## LU041117_V1 LU041117_V2 AH060617_V1 AH060617_V2 ER121316_V1
## A1BG-AS1 5.581169 0.000000 0.00000 0.000000 12.3731326
## A2M-AS1 3.720779 0.000000 0.00000 13.096098 4.4543277
## A2ML1-AS1 0.000000 2.804077 0.00000 0.000000 0.9898506
## A2ML1-AS2 0.000000 0.000000 0.00000 0.000000 0.0000000
## AADACL2-AS1 5.581169 0.000000 0.00000 4.365366 7.4238795
## AATBC 5.581169 21.030574 64.49022 65.480490 16.8274603
## ER121316_V2 OC012517_V1 OC012517_V2
## A1BG-AS1 4.181338 9.622995 0
## A2M-AS1 0.000000 5.498854 0
## A2ML1-AS1 0.000000 0.000000 0
## A2ML1-AS2 0.000000 0.000000 0
## AADACL2-AS1 8.362676 4.124141 0
## AATBC 8.362676 20.620704 0annotation <- colData(dds)
annotation## DataFrame with 28 rows and 9 columns
## SampleID Age Sex BMI SampleName Visit
## <factor> <integer> <factor> <numeric> <factor> <factor>
## AL101116_V1 AL101116_V1 83 F 20.4 AL101116_V1 Visit1
## AL101116_V2 AL101116_V2 83 F 19.7 AL101116_V2 Visit2
## AE032117_V1 AE032117_V1 74 F 25.3 AE032117_V1 Visit1
## AE032117_V2 AE032117_V2 74 F 25.1 AE032117_V2 Visit2
## NM012517_V1 NM012517_V1 65 F 21.7 NM012517_V1 Visit1
## ... ... ... ... ... ... ...
## AH060617_V2 AH060617_V2 70 M 28.7 AH060617_V2 Visit2
## ER121316_V1 ER121316_V1 39 F 68.9 ER121316_V1 Visit1
## ER121316_V2 ER121316_V2 39 F 67 ER121316_V2 Visit2
## OC012517_V1 OC012517_V1 56 M 22.2 OC012517_V1 Visit1
## OC012517_V2 OC012517_V2 56 M 20.8 OC012517_V2 Visit2
## PID Group sizeFactor
## <factor> <factor> <numeric>
## AL101116_V1 AL101116 HFrEF 0.928635569369158
## AL101116_V2 AL101116 HFrEF 3.6910497738802
## AE032117_V1 AE032117 HFrEF 4.47858967473624
## AE032117_V2 AE032117 HFrEF 7.18511494294293
## NM012517_V1 NM012517 HFrEF 3.09222757789431
## ... ... ... ...
## AH060617_V2 AH060617 HFpEF 0.22907586634865
## ER121316_V1 ER121316 HFrEF 2.02050692190161
## ER121316_V2 ER121316 HFrEF 0.239157904149093
## OC012517_V1 OC012517 HFrEF 0.727424237208874
## OC012517_V2 OC012517 HFrEF 0.314777823808078ContrApption(data = d, annotation = annotation, idCol = "SampleID", groupCol = "Group")## Input to asJSON(keep_vec_names=TRUE) is a named vector. In a future version of jsonlite, this option will not be supported, and named vectors will be translated into arrays instead of objects. If you want JSON object output, please use a named list instead. See ?toJSON.# need to make uuids before I can have more than one on the same page
ContrApption(data = d, annotation = annotation, idCol = "SampleID", groupCol = "Visit")## Input to asJSON(keep_vec_names=TRUE) is a named vector. In a future version of jsonlite, this option will not be supported, and named vectors will be translated into arrays instead of objects. If you want JSON object output, please use a named list instead. See ?toJSON.Sure why not?